VS 2PCG is indeed like that. And despite the price of the base box, it's the cheapest there is if you want a full set (as in, as many copies of each card as you can include in a deck), since you need only 1 box to get it (the others need 2 or 3 boxes for that). However, the cards and tokens are of very poor quality; you'll need to sleeve the cards right away if you want them to stay in good shape (which doesn't sound promising with a 6-year-old). With the others (possibly VS as well, I don't know), you can skip deckbuilding at the start, since the boxes have enough cards to make at least 2 decks and lists are included. You could go with Star Wars (deckbuilding is simpler than the others, too, once you want to go into it).
By the way, I've tried out My Little Pony CCG and it's designed well (though the youngest players I've met are 15). If your son likes the theme, you could go with that (there are starter decks if you don't want to go into deckbuilding).